Re: [Gmod-ajax] Perl lib version question

[Zhiliang Hu <hu...@an...>]

Hi Colin,

Yes, upon my first run of 'setup.sh' of the new download, it complained 
about "... perl v5.12 ...not compatible with perl v5.30" or something like 
that. My ssh window does not scroll back that far.  I thought I read 
something similar on jbrowse web site but can't locate it this moment.

Zhiliang


On Tue, 14 Jul 2020, Colin wrote:

> Date: Tue, 14 Jul 2020 16:39:57 -0400
> From: Colin <col...@gm...>
> To: Zhiliang Hu <hu...@an...>
> Cc: gmod-ajax <gmo...@li...>
> Subject: Re: [Gmod-ajax] Perl lib version question
> 
> I am not really sure but I wanted to revisit your other email
>
>> As needed by new JBrowse, I installed perl 5.30 into the
> /usr/local/bin/ location (my /usr/bin/ location has perl 5.16)
>
> There is no requirement to use a new version of perl with newer versions of
> JBrowse as far as I know, we should be backwards compatible with pretty old
> versions of perl
>
> Did you see something that seemed to need an upgraded perl?
>
>
> -Colin
>
> On Tue, Jul 14, 2020 at 4:10 PM Zhiliang Hu <hu...@an...> wrote:
>
>> Thank you Colin!  This was an eye openning for me to cpanm... My ran of
>> "cpanm Bio::Perl@1.7.2" seemed an success.
>>
>> I was able to get rid of multiple "Segmentation fault (core dumped)"
>> by changing the line in 'setup.sh' where perl was called with a full path:
>> "have_db=`/usr/local/bin/perl -MConfig=myconfig -e".  The setup was a
>> success!
>>
>> Now I am getting "Segmentation fault (core dumped)" running
>> "flatfile-to-json.pl", even after I changed its "#!/usr/bin/env perl" line
>> to "#!/usr/local/bin/perl".
>>
>> Any suggestion please?
>>
>> Zhiliang
>>
>>
>> On Tue, 14 Jul 2020, Colin wrote:
>>
>>> Date: Tue, 14 Jul 2020 13:03:54 -0400
>>> From: Colin <col...@gm...>
>>> To: Zhiliang Hu <hu...@an...>
>>> Cc: gmod-ajax <gmo...@li...>
>>> Subject: Re: [Gmod-ajax] Perl lib version question
>>>
>>> If you have cpanm installed globally on your system you can try to
>> manually
>>> run this command
>>>
>>> cpanm Bio::Perl@1.7.2
>>>
>>> A similar thing can likely be done with the plain cpan executable also,
>>> possibly this
>>>
>>> cpan CJFIELDS/BioPerl-1.007002.tar.gz
>>>
>>>
>>> We require 1.7.2 because later versions really significantly modified the
>>> BioPerl ecosystem (see changelog here
>>> https://github.com/bioperl/bioperl-live/blob/master/Changes)
>>>
>>>
>>> -Colin
>>>
>>>
>>> On Tue, Jul 14, 2020 at 11:59 AM Zhiliang Hu <hu...@an...>
>> wrote:
>>>
>>>>
>>>> Thanks Colin for addressing the issue.  I took the path to reinstall the
>>>> JBrowse.  As needed by new JBrowse, I installed perl 5.30 into the
>>>> /usr/local/bin/ location (my /usr/bin/ location has perl 5.16)
>>>>
>>>> My newly downloaded JBrowse setup.sh (at a location different from
>>>> previous installations; on a RedHat CentOS 7 system) got complains like:
>>>>
>>>> Installing Perl prerequisites ...
>>>> + bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2
>>>> ./setup.sh: line 142: 10708 Segmentation fault      (core dumped)
>>>>
>>>> I understand it might be caused by multiple perl versions on my system
>> but
>>>> by cleaning my shell environment PERLLIB/ PERL5LIB didn't help. I wonder
>>>> is there alternative ways to install "Bio::Perl@1.7.2" (actually which
>>>> modules?).
>>>>
>>>> I searched for old JBrowse troubleshooting and did:
>>>>> sudo yum groupinstall "Development Tools"
>>>>> sudo yum install libpng-devel gd-devel zlib-devel
>> perl-ExtUtils-MakeMaker
>>>> and it didn't help.
>>>>
>>>> Any further suggestion please? (I know on this RH Centos7 system there
>> are
>>>> perl GD, Zlib, and libpng installed but how to make the JBrowse setup
>> know
>>>> where they are?)
>>>>
>>>> Zhiliang
>>>>
>>>> On Wed, 3 Jun 2020, Colin wrote:
>>>>
>>>>> Date: Wed, 3 Jun 2020 20:34:24 -0400
>>>>> From: Colin <col...@gm...>
>>>>> To: Zhiliang Hu <hu...@an...>
>>>>> Cc: gmod-ajax <gmo...@li...>
>>>>> Subject: Re: [Gmod-ajax] Perl lib version question
>>>>>
>>>>> There have been a couple people experiencing this lately. I am not
>>>> exactly
>>>>> sure why, maybe it is related people who have older versions of jbrowse
>>>>> upgrading to perl 5.30+.
>>>>>
>>>>> JBrowse generally installs all it's perl dependencies to a folder
>> inside
>>>>> JBROWSE_ROOT/extlib
>>>>>
>>>>> I would try rm -rf extlib, maybe also ~/.cpanm and ~/.cpan, then re-run
>>>>> setup.sh
>>>>>
>>>>> Here is a chat log of a user on our chat that also did these steps but
>> it
>>>>> was  on macOS
>>>>>
>>>>>> * nuke all traces of perl in /User (brew, .cpan, .cpanm etc.)
>>>>>> * `sudo installer -pkg
>>>>>
>>>>
>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>>>> -target` - allows  Extern_H compile problem to  pass
>>>>>> * use `cpan` to `install JSON::XS` (for some reason the dependency
>> won't
>>>>> install during setup.sh)
>>>>>> * run `setup.sh`
>>>>>
>>>>>
>>>>>
>>>>> -Colin
>>>>>
>>>>> On Wed, Jun 3, 2020 at 7:37 PM Zhiliang Hu <hu...@an...>
>> wrote:
>>>>>
>>>>>> When I tried to load data to JBrowse, I got the following complain:
>>>>>>
>>>>>> Perl lib version (5.16.3) doesn't match executable
>>>>>> '/home/apache/doc/jbrowse/bin/flatfile-to-json.pl' version (v5.30.0)
>> at
>>>>>> /usr/lib64/perl5/Config.pm line 60.
>>>>>> Compilation failed in require at /usr/lib64/perl5/lib.pm line 6.
>>>>>>
>>>>>> In cpan I did "reload cpan" and "install lib" and it says:
>>>>>>
>>>>>>    lib is up to date (0.63)
>>>>>>
>>>>>> I am at a lost as how to update my "perl lib". Any advice please?
>>>>>>
>>>>>> Zhiliang
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Gmod-ajax mailing list
>>>>>> Gmo...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>
>>>>>
>>>>
>>>
>>
>